X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fdbsources%2FPdb.java;h=c75a36f9d9c78b8a5913572943171802c9c66ab0;hb=c394157681d10261bd6f7883b19eaf88d6784609;hp=b2529003513bcd053df3fb816cc16e17734fef0f;hpb=47168f025aefdaa044802bd5f8f510ffe43a4808;p=jalview.git

diff --git a/src/jalview/ws/dbsources/Pdb.java b/src/jalview/ws/dbsources/Pdb.java
index b252900..c75a36f 100644
--- a/src/jalview/ws/dbsources/Pdb.java
+++ b/src/jalview/ws/dbsources/Pdb.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -20,26 +20,23 @@
  */
 package jalview.ws.dbsources;
 
-import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
 import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.DBRefSource;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
+import jalview.io.FormatAdapter;
+import jalview.util.MessageManager;
+import jalview.ws.ebi.EBIFetchClient;
+import jalview.ws.seqfetcher.DbSourceProxy;
 
 import java.util.ArrayList;
 import java.util.List;
 import java.util.Vector;
 
-import MCview.PDBChain;
-import MCview.PDBfile;
-
 import com.stevesoft.pat.Regex;
 
-import jalview.datamodel.AlignmentI;
-import jalview.io.FormatAdapter;
-import jalview.ws.ebi.EBIFetchClient;
-import jalview.ws.seqfetcher.DbSourceProxy;
-
 /**
  * @author JimP
  * 
@@ -138,16 +135,16 @@ public class Pdb extends EbiFileRetrievedProxy implements DbSourceProxy
               jalview.io.AppletFormatAdapter.FILE, "PDB");
       if (pdbfile != null)
       {
-        List<SequenceI> toremove=new ArrayList<SequenceI>();
+        List<SequenceI> toremove = new ArrayList<SequenceI>();
         for (SequenceI pdbcs : pdbfile.getSequences())
         {
           String chid = null;
           // Mapping map=null;
-          for (PDBEntry pid : (Vector<PDBEntry>) pdbcs.getPDBId())
+          for (PDBEntry pid : pdbcs.getPDBId())
           {
             if (pid.getFile() == file)
             {
-              chid = (String) pid.getProperty().get("CHAIN");
+              chid = pid.getChainCode();
 
             }
             ;
@@ -183,21 +180,28 @@ public class Pdb extends EbiFileRetrievedProxy implements DbSourceProxy
           }
           else
           {
-            // mark this sequence to be removed from the alignment 
+            // mark this sequence to be removed from the alignment
             // - since it's not from the right chain
             toremove.add(pdbcs);
           }
         }
-        // now remove marked sequences 
-        for (SequenceI pdbcs:toremove) {
+        // now remove marked sequences
+        for (SequenceI pdbcs : toremove)
+        {
           pdbfile.deleteSequence(pdbcs);
+          if (pdbcs.getAnnotation()!=null)
+          {
+            for (AlignmentAnnotation aa: pdbcs.getAnnotation())
+            {
+              pdbfile.deleteAnnotation(aa);
+            }
+          }
         }
       }
-      
+
       if (pdbfile == null || pdbfile.getHeight() < 1)
       {
-        throw new Exception("No PDB Records for " + id + " chain "
-                + ((chain == null) ? "' '" : chain));
+        throw new Exception(MessageManager.formatMessage("exception.no_pdb_records_for_chain", new String[]{id, ((chain == null) ? "' '" : chain)}));
       }
 
     } catch (Exception ex) // Problem parsing PDB file